For the repairs use hardwood plywood, at least 18mm thick, screwed to the joists. If your original floor boards are say 25mm thick, the plywood can be lifted 3mm by adding strips of oil-tempered Masonite or hardboard packer strips to the tops of the joists, or by 5.5mm by adding strips of 5.5mm hardwood plywood. Alternatively an additional top skin of 5.5mm ("1/4 in") hardwood plywood can be loosely fixed to the top of the plywood patches (only a few nails are needed for this). Differences of a couple of millimetres can be taken out with a skim (see below)
If the planked floor is reasonably level you can get away with nailing sheets of 5.5mm hardwood plywood over the top of it - 19 or 22mm ring shank clouts at 100mm centres ( i.e. 325 nails per sheet). If the planks are a bit less level you might need 12mm hardwood plywood. Either way I'd use a self levelling compound over the plywood to smooth out any minor sunken areas
